MolNFT v1 · #41164 · protein
Estrogen receptor alpha lbd in complex with an affinity-selected corepressor peptide
2JFA: “Estrogen receptor alpha lbd in complex with an affinity-selected corepressor peptide”. X-ray diffraction, 2 ligands (RAL, SO4), 5 pockets (best druggability 0.75). MolNFT v1 #41164 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2JFA
- Type
- protein
- Length
- 474 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Corepressor peptide
- UniProt
- P03372
- Ligands
- RAL, SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 221 | 72% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 223 | 70% helix, 4% strand | P03372 |
| P, Q | Corepressor peptide | protein | 15 | 80% helix, 0% strand | — |
Ligands and binding sites
- RAL · Raloxifene · ligand · 2 copies · chains A, P, B, Q
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.75 | 0.81 | 83 | RAL |
| 2 | 427 | 0.72 | 0.82 | 46 | RAL |
| 3 | 99 | 0.66 | 0.90 | 20 | empty |
| 4 | 93 | 0.64 | 0.90 | 23 | empty |
| 5 | 217 | 0.59 | 0.80 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1597 Ų buried · 26 hydrogen bonds · protein-protein
- A–P · 519 Ų buried · 4 hydrogen bonds · protein-protein
- B–Q · 500 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 2JFA · Estrogen receptor alpha lbd in complex with an affinity-selected corepressor peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P03372
- Elsewhere: RCSB PDB 2JFA · PDBe 2JFA · UniProt P03372
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